Dataset Information

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

ABSTRACT: Patterns observed by examining the evolutionary relationships among proteins of common origin can reveal the structural and functional importance of specific residue positions. In particular, amino acids that are highly conserved (i.e., their positions evolve at a slower rate than other positions) are particularly likely to be of biological importance, for example, for ligand binding. ConSurf is a bioinformatics tool for accurately estimating the evolutionary rate of each position in a protein family. Here we introduce a new release of ConSurf-DB, a database of precalculated ConSurf evolutionary conservation profiles for proteins of known structure. ConSurf-DB provides high-accuracy estimates of the evolutionary rates of the amino acids in each protein. A reliable estimate of a query protein's evolutionary rates depends on having a sufficiently large number of effective homologues (i.e., nonredundant yet sufficiently similar). With current sequence data, ConSurf-DB covers 82% of the PDB proteins. It will be updated on a regular basis to ensure that coverage remains high-and that it might even increase. Much effort was dedicated to improving the user experience. The repository is available at https://consurfdb.tau.ac.il/. BROADER AUDIENCE: By comparing a protein to other proteins of similar origin, it is possible to determine the extent to which each amino acid position in the protein evolved slowly or rapidly. A protein's evolutionary profile can provide valuable insights: For example, amino acid positions that are highly conserved (i.e., evolved slowly) are particularly likely to be of structural and/or functional importance, for example, for ligand binding and catalysis. We introduce here a new and improved version of ConSurf-DB, a continually updated database that provides precalculated evolutionary profiles of proteins with known structure.

SUBMITTER: Ben Chorin A

PROVIDER: S-EPMC6933843 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

Ben Chorin Adi A Masrati Gal G Kessel Amit A Narunsky Aya A Sprinzak Josef J Lahav Shlomtzion S Ashkenazy Haim H Ben-Tal Nir N

Protein science : a publication of the Protein Society 20191122 1

Patterns observed by examining the evolutionary relationships among proteins of common origin can reveal the structural and functional importance of specific residue positions. In particular, amino acids that are highly conserved (i.e., their positions evolve at a slower rate than other positions) are particularly likely to be of biological importance, for example, for ligand binding. ConSurf is a bioinformatics tool for accurately estimating the evolutionary rate of each position in a protein f ...[more]

PMID: 31702846

Similar Datasets

Project description:The invertase gene family in plants is composed of two subfamilies of enzymes, namely, acid- and neutral/alkaline invertases (cytosolic invertase, CIN). Both can irreversibly cleave sucrose into fructose and glucose, which are thought to play key roles in carbon metabolism and plant growth. CINs are widely found in plants, but little is reported about this family. In this paper, a comparative genomic approach was used to analyze the CIN gene family in Solanum, including Solanumtuberosum, Solanumlycopersicum, Solanumpennellii, Solanumpimpinellifolium, and Solanummelongena. A total of 40 CINs were identified in five Solanum plants, and sequence features, phylogenetic relationships, motif compositions, gene structure, collinear relationship, and expression profile were further analyzed. Sequence analysis revealed a remarkable conservation of CINs in sequence length, gene number, and molecular weight. The previously verified four amino acid residues (D188, E414, Arg430, and Ser547) were also observed in 39 out of 40 CINs in our study, showing to be deeply conserved. The CIN gene family could be distinguished into groups α and β, and α is further subdivided into subgroups α1 and α2 in our phylogenetic tree. More remarkably, each species has an average of four CINs in the α and β groups. Marked interspecies conservation and collinearity of CINs were also further revealed by chromosome mapping. Exon-intron configuration and conserved motifs were consistent in each of these α and β groups on the basis of in silico analysis. Expression analysis indicated that CINs were constitutively expressed and share similar expression profiles in all tested samples from S. tuberosum and S.lycopersicum. In addition, in CIN genes of the tomato and potato in response to abiotic and biotic stresses, phytohormones also performed. Overall, CINs in Solanum were encoded by a small and highly conserved gene family, possibly reflecting structural and functional conservation in Solanum. These results lay the foundation for further expounding the functional characterization of CIN genes and are also significant for understanding the evolutionary profiling of the CIN gene family in Solanum.

Dataset Information

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

Publications

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets